Read the Docs build information
Build id: 1625145
Project: icb-scanpy
Version: 2554
Commit: 29c6a08f7a0e1af301ad6b8d0b26e7b917ef1971
Date: 2023-07-27T13:49:50.828431Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-07-27T13:50:35.988918Z, end-time: 2023-07-27T13:50:37.227721Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-07-27T13:50:37.483876Z, end-time: 2023-07-27T13:50:38.149626Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/2554/head:external-2554
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/2554/head -> external-2554

[rtd-command-info] start-time: 2023-07-27T13:50:38.419603Z, end-time: 2023-07-27T13:50:38.632321Z, duration: 0, exit-code: 0
git checkout --force 29c6a08f7a0e1af301ad6b8d0b26e7b917ef1971
Note: switching to '29c6a08f7a0e1af301ad6b8d0b26e7b917ef1971'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 29c6a08 Merge branch 'master' into fix-rank-gene-groups-violin-gene-symbols

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git clean -d -f -f


[rtd-command-info] start-time: 2023-07-27T13:50:39.371561Z, end-time: 2023-07-27T13:50:39.467129Z, duration: 0, exit-code: 0
git submodule sync


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git submodule update --init --force docs/tutorials
Submodule 'docs/tutorials' (https://github.com/scverse/scanpy-tutorials.git) registered for path 'docs/tutorials'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/tutorials'...
Submodule path 'docs/tutorials': checked out 'ba8e433ea7c0fc3b1e1e482ecc2e1dd5f59a9d9d'

[rtd-command-info] start-time: 2023-07-27T13:50:53.072016Z, end-time: 2023-07-27T13:50:53.148734Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: '3.9'
sphinx:
  configuration: docs/conf.py
python:
  install:
  - method: pip
    path: .
    extra_requirements:
    - doc
    - leiden
submodules:
  include:
     - "docs/tutorials"

[rtd-command-info] start-time: 2023-07-27T13:50:59.211780Z, end-time: 2023-07-27T13:50:59.283370Z, duration: 0, exit-code: 0
asdf global python 3.9.17


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.17.final.0-64 in 687ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2554, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2023-07-27T13:51:01.315583Z, end-time: 2023-07-27T13:51:12.739367Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2554/lib/python3.9/site-packages (21.2.3)
Collecting pip
  Downloading pip-23.2.1-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2554/lib/python3.9/site-packages (57.4.0)
Collecting setuptools
  Downloading setuptools-68.0.0-py3-none-any.whl (804 kB)
Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 57.4.0
    Uninstalling setuptools-57.4.0:
      Successfully uninstalled setuptools-57.4.0
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-23.2.1 setuptools-68.0.0

[rtd-command-info] start-time: 2023-07-27T13:51:13.151328Z, end-time: 2023-07-27T13:51:20.501828Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2554/lib/python3.9/site-packages (from sphinx<2) (68.0.0)
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Collecting urllib3<3,>=1.21.1 (from requests>=2.0.0->sphinx<2)
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Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=41509355eb80ab1d832c1f7d24f3caabb545e28b89f41b7e165fb9dc618d6ee5
  Stored in directory: /tmp/pip-ephem-wheel-cache-9pjivam_/wheels/44/dc/c7/e89296d3612588db0aa6545ee3305c23b7a48b3a9922916e1f
Successfully built mock
Installing collected packages: snowballstemmer, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.3 Pygments-2.15.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-10.0.0 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.4

[rtd-command-info] start-time: 2023-07-27T13:51:20.812352Z, end-time: 2023-07-27T13:52:53.726518Z, duration: 92, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,leiden]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554
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  Building wheel for pynndescent (setup.py): finished with status 'done'
  Created wheel for pynndescent: filename=pynndescent-0.5.10-py3-none-any.whl size=55624 sha256=fc23329830d1fa6e184494bba0d4e9148d61d20536e1a3333348f45adcdd0440
  Stored in directory: /tmp/pip-ephem-wheel-cache-i42hi864/wheels/12/f9/4d/ec5ad1c823c710fcc4473669fdcffc8891f4bc398c841af22e
Successfully built umap-learn scanpy session-info pynndescent
Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, pickleshare, fastjsonschema, executing, backcall, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, tinycss2, threadpoolctl, tabulate, stdlib_list, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, rpds-py, pyzmq, pyyaml, python-dateutil, pyparsing, psutil, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, networkx, nest-asyncio, natsort, mistune, mdurl, llvmlite, kiwisolver, jupyterlab-pygments, joblib, igraph, greenlet, fonttools, defusedxml, decorator, debugpy, cycler, click, bleach, attrs, asttokens, accessible-pygments, stack-data, sqlalchemy, session-info, scipy, referencing, patsy, pandas, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib-resources, importlib-metadata, h5py, contourpy, comm, beautifulsoup4, statsmodels, sphinx, scikit-learn, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, ipython, anndata, sphinxext-opengraph, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, seaborn, scanpydoc, pynndescent, pydata-sphinx-theme, myst-parser, jsonschema, ipykernel, umap-learn, sphinx-book-theme, nbformat, scanpy, nbclient, nbconvert, jupyter-cache, nbsphinx, myst-nb
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.6
    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
Successfully installed accessible-pygments-0.0.4 anndata-0.9.2 asttokens-2.2.1 attrs-23.1.0 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 click-8.1.6 comm-0.1.3 contourpy-1.1.0 cycler-0.11.0 debugpy-1.6.7 decorator-5.1.1 defusedxml-0.7.1 executing-1.2.0 fastjsonschema-2.18.0 fonttools-4.41.1 greenlet-2.0.2 h5py-3.9.0 igraph-0.10.6 importlib-metadata-6.8.0 importlib-resources-6.0.0 ipykernel-6.25.0 ipython-8.14.0 jedi-0.18.2 joblib-1.3.1 jsonschema-4.18.4 jsonschema-specifications-2023.7.1 jupyter-cache-0.6.1 jupyter-client-8.3.0 jupyter-core-5.3.1 jupyterlab-pygments-0.2.2 kiwisolver-1.4.4 leidenalg-0.10.1 llvmlite-0.40.1 markdown-it-py-2.2.0 matplotlib-3.7.2 matplotlib-inline-0.1.6 mdit-py-plugins-0.3.5 mdurl-0.1.2 mistune-3.0.1 myst-nb-0.17.2 myst-parser-0.18.1 natsort-8.4.0 nbclient-0.7.4 nbconvert-7.7.3 nbformat-5.9.1 nbsphinx-0.9.2 nest-asyncio-1.5.6 networkx-3.1 numba-0.57.1 numpy-1.24.4 pandas-2.0.3 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-3.9.1 prompt-toolkit-3.0.39 psutil-5.9.5 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.13.3 pynndescent-0.5.10 pyparsing-3.0.9 python-dateutil-2.8.2 pytz-2023.3 pyyaml-6.0.1 pyzmq-25.1.0 referencing-0.30.0 rpds-py-0.9.2 scanpy-0.1.dev57+g29c6a08 scanpydoc-0.9.4 scikit-learn-1.3.0 scipy-1.11.1 seaborn-0.12.2 session-info-1.0.0 soupsieve-2.4.1 sphinx-4.5.0 sphinx-autodoc-typehints-1.19.1 sphinx-book-theme-1.0.1 sphinx-copybutton-0.5.2 sphinx-design-0.4.1 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxext-opengraph-0.8.2 sqlalchemy-2.0.19 stack-data-0.6.2 statsmodels-0.14.0 stdlib_list-0.9.0 tabulate-0.9.0 texttable-1.6.7 threadpoolctl-3.2.0 tinycss2-1.2.1 tornado-6.3.2 tqdm-4.65.0 traitlets-5.9.0 typing-extensions-4.7.1 tzdata-2023.3 umap-learn-0.5.3 wcwidth-0.2.6 webencodings-0.5.1 zipp-3.16.2

[rtd-command-info] start-time: 2023-07-27T13:52:57.422028Z, end-time: 2023-07-27T13:52:57.476384Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
import importlib.util
import inspect
import re
import subprocess
from pathlib import Path
from datetime import datetime
from typing import Any

import matplotlib  # noqa
from packaging.version import parse as parse_version

# Don’t use tkinter agg when importing scanpy → … → matplotlib
matplotlib.use('agg')

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')]
import scanpy  # noqa

on_rtd = os.environ.get('READTHEDOCS') == 'True'

# -- General configuration ------------------------------------------------


nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
needs_sphinx = '4.0'  # Nicer param docs
suppress_warnings = [
    'ref.citation',
    'myst.header',  # https://github.com/executablebooks/MyST-Parser/issues/262
]

# General information
project = 'Scanpy'
author = 'Scanpy development team'
repository_url = "https://github.com/scverse/scanpy"
copyright = f'{datetime.now():%Y}, the Scanpy development team.'
version = scanpy.__version__.replace('.dirty', '')

# Bumping the version updates all docs, so don't do that
if parse_version(version).is_devrelease:
    parsed = parse_version(version)
    version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev"

release = version

# default settings
templates_path = ['_templates']
master_doc = 'index'
default_role = 'literal'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']

extensions = [
    'myst_nb',
    'sphinx_copybutton',
    'sphinx.ext.autodoc',
    'sphinx.ext.intersphinx',
    'sphinx.ext.doctest',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.napoleon',
    'sphinx.ext.autosummary',
    'sphinx.ext.linkcode',
    'sphinx.ext.extlinks',
    'matplotlib.sphinxext.plot_directive',
    'sphinx_autodoc_typehints',  # needs to be after napoleon
    'scanpydoc.autosummary_generate_imported',
    'scanpydoc.definition_list_typed_field',
    'sphinx_design',
    'sphinxext.opengraph',
    *[p.stem for p in (HERE / 'extensions').glob('*.py')],
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = 'bysource'
# autodoc_default_flags = ['members']
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True  # having a separate entry generally helps readability
napoleon_use_param = True
napoleon_custom_sections = [('Params', 'Parameters')]
todo_include_todos = False
api_dir = HERE / 'api'  # function_images
myst_enable_extensions = [
    "amsmath",
    "colon_fence",
    "deflist",
    "dollarmath",
    "html_image",
    "html_admonition",
]
myst_url_schemes = ("http", "https", "mailto")
nb_output_stderr = "remove"
nb_execution_mode = "off"
nb_merge_streams = True


ogp_site_url = "https://scanpy.readthedocs.io/en/stable/"
ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg"

typehints_defaults = 'braces'

scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/'

pygments_style = "default"
pygments_dark_style = "native"

intersphinx_mapping = dict(
    anndata=('https://anndata.readthedocs.io/en/stable/', None),
    bbknn=('https://bbknn.readthedocs.io/en/latest/', None),
    cycler=('https://matplotlib.org/cycler/', None),
    h5py=('https://docs.h5py.org/en/stable/', None),
    ipython=('https://ipython.readthedocs.io/en/stable/', None),
    leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None),
    louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None),
    matplotlib=('https://matplotlib.org/stable/', None),
    networkx=('https://networkx.org/documentation/stable/', None),
    numpy=('https://numpy.org/doc/stable/', None),
    pandas=('https://pandas.pydata.org/pandas-docs/stable/', None),
    pytest=('https://docs.pytest.org/en/latest/', None),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/', None),
    seaborn=('https://seaborn.pydata.org/', None),
    sklearn=('https://scikit-learn.org/stable/', None),
    scanpy_tutorials=(scanpy_tutorials_url, None),
)


# -- Options for HTML output ----------------------------------------------

html_theme = "sphinx_book_theme"
html_theme_options = {
    "repository_url": repository_url,
    "use_repository_button": True,
    "logo_only": True,
    "show_toc_level": 4,  # show all levels in the sidebar
}
html_static_path = ['_static']
html_css_files = ["css/override.css"]
html_show_sphinx = False
html_logo = '_static/img/Scanpy_Logo_BrightFG.svg'
html_title = "scanpy"


def setup(app):
    """App setup hook."""
    # TODO: fix all warnings in a future PR
    # Many come from the tutorials, like the workshop directory
    # which is not included in the docs
    #     app.warningiserror = on_rtd
    app.add_config_value(
        "recommonmark_config",
        {
            "auto_toc_tree_section": "Contents",
            "enable_auto_toc_tree": True,
            "enable_math": True,
            "enable_inline_math": False,
            "enable_eval_rst": True,
        },
        True,
    )


# -- Options for other output formats ------------------------------------------

htmlhelp_basename = f'{project}doc'
doc_title = f'{project} Documentation'
latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')]
man_pages = [(master_doc, project, doc_title, [author], 1)]
texinfo_documents = [
    (
        master_doc,
        project,
        doc_title,
        author,
        project,
        'One line description of project.',
        'Miscellaneous',
    )
]


# -- Suppress link warnings ----------------------------------------------------

qualname_overrides = {
    "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric",
    # If the docs are built with an old version of numpy, this will make it work:
    "numpy.random.RandomState": "numpy.random.mtrand.RandomState",
    "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot",
    "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot",
    "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin",
    "pandas.core.series.Series": "pandas.Series",
}

nitpick_ignore = [
    # Will probably be documented
    ('py:class', 'scanpy._settings.Verbosity'),
    # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
    ('py:class', 'seaborn.ClusterGrid'),
    # Won’t be documented
    ('py:class', 'scanpy.plotting._utils._AxesSubplot'),
    ('py:class', 'scanpy._utils.Empty'),
    ('py:class', 'numpy.random.mtrand.RandomState'),
    # Will work once scipy 1.8 is released
    ('py:class', 'scipy.sparse.base.spmatrix'),
    ('py:class', 'scipy.sparse.csr.csr_matrix'),
]

# Options for plot examples

plot_include_source = True
plot_formats = [("png", 90)]
plot_html_show_formats = False
plot_html_show_source_link = False
plot_working_directory = HERE.parent  # Project root

# Linkcode config


def git(*args):
    return subprocess.check_output(["git", *args]).strip().decode()


# https://github.com/DisnakeDev/disnake/blob/7853da70b13fcd2978c39c0b7efa59b34d298186/docs/conf.py#L192
# Current git reference. Uses branch/tag name if found, otherwise uses commit hash
git_ref = None
try:
    git_ref = git("name-rev", "--name-only", "--no-undefined", "HEAD")
    git_ref = re.sub(r"^(remotes/[^/]+|tags)/", "", git_ref)
except Exception:
    pass

# (if no name found or relative ref, use commit hash instead)
if not git_ref or re.search(r"[\^~]", git_ref):
    try:
        git_ref = git("rev-parse", "HEAD")
    except Exception:
        git_ref = "master"

# https://github.com/DisnakeDev/disnake/blob/7853da70b13fcd2978c39c0b7efa59b34d298186/docs/conf.py#L192
_module_path = os.path.dirname(importlib.util.find_spec("scanpy").origin)  # type: ignore


def linkcode_resolve(domain, info):
    if domain != "py":
        return None

    try:
        obj: Any = sys.modules[info["module"]]
        for part in info["fullname"].split("."):
            obj = getattr(obj, part)
        obj = inspect.unwrap(obj)

        if isinstance(obj, property):
            obj = inspect.unwrap(obj.fget)  # type: ignore

        path = os.path.relpath(inspect.getsourcefile(obj), start=_module_path)  # type: ignore
        src, lineno = inspect.getsourcelines(obj)
    except Exception:
        return None

    path = f"{path}#L{lineno}-L{lineno + len(src) - 1}"
    return f"{repository_url}/blob/{git_ref}/scanpy/{path}"


# extlinks config
extlinks = {
    "issue": ("https://github.com/scverse/scanpy/issues/%s", "issue%s"),
    "pr": ("https://github.com/scverse/scanpy/pull/%s", "pr%s"),
    "tutorial": (
        "https://github.com/scverse/scanpy-tutorials/%s.ipynb",
        "tutorial: %s",
    ),
}




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "2554",
    'version_slug': "2554",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy',
    'name': u'scanpy',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'scverse',
    'proxied_api_host': '/_',
    'github_repo': 'scanpy',
    'github_version': '29c6a08f7a0e1af301ad6b8d0b26e7b917ef1971',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '29c6a08f7a0e1af301ad6b8d0b26e7b917ef1971',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '29c6a08f7a0e1af301ad6b8d0b26e7b917ef1971',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '29c6a08f',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'external' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'https://github.com/scverse/scanpy/pull/2554'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/1625145/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2023-07-27T13:52:57.725398Z, end-time: 2023-07-27T13:57:12.700167Z, duration: 254, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v4.5.0
loading translations [en]... done
making output directory... done
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['amsmath', 'colon_fence', 'deflist', 'dollarmath', 'html_image', 'html_admonition'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
myst-nb v0.17.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/_readthedocs/.jupyter_cache
loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv...
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[autosummary] generating autosummary for: _tutorials.md, api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., tutorials/scanpy_workshop/day2_01_DE_Colabs.ipynb, tutorials/scanpy_workshop/day2_01_DifferentialExpression.ipynb, tutorials/scanpy_workshop/day2_02_GSEA_Colabs.ipynb, tutorials/scanpy_workshop/day2_02_GeneSetEnrichmentAnalysis.ipynb, tutorials/scanpy_workshop/day2_03_RNAvelocity.ipynb, tutorials/spatial/basic-analysis.ipynb, tutorials/spatial/integration-scanorama.ipynb, tutorials/tutorial_pearson_residuals.ipynb, tutorials/visualizing-marker-genes.rst, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst
building [mo]: targets for 0 po files that are out of date
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/scanpy/plotting/_tools/scatterplots.py:396: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
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WARNING: Package 'fa2' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2' (`pip install fa2`).
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/scanpy/plotting/_tools/scatterplots.py:396: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/scanpy/plotting/_tools/scatterplots.py:396: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2554/lib/python3.9/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2554/lib/python3.9/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2554/lib/python3.9/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2554/lib/python3.9/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
  @numba.jit()
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  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/scanpy/plotting/_tools/scatterplots.py:396: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
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WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2554/scanpy/plotting/_dotplot.py:747: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
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WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
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WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
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copying static files... done
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build succeeded, 37 warnings.

The HTML pages are in ../_readthedocs/html.
Updating searchtools for Read the Docs search...